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(-) Description

Title :  XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH XYLOBIO-DEOXYNOJIRIMYCIN AT PH 5.8
 
Authors :  T. M. Gloster, S. J. Williams, S. Roberts, C. A. Tarling, J. Wicki S, G. Withers, G. J. Davies
Date :  31 Mar 04  (Deposition) - 16 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.03
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoside Hydrolase Family 10, Xylanase, Xylan Degradation, Deoxynojirimycin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Gloster, S. J. Williams, S. Roberts, C. A. Tarling, J. Wicki, S. G. Withers, G. J. Davies
Atomic Resolution Analyses Of The Binding Of Xylobiose-Derived Deoxynojirimycin And Isofagomine To Xylanase Xyn10A
Chem. Commun. (Camb. ) V. 16 1794 2004
PubMed-ID: 15306887  |  Reference-DOI: 10.1039/B405152A

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE A
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: STREPTOMYCES LIVIDANS
    Expression System Strain: IAF 19
    Expression System Taxid: 1916
    Fragment: CATALYTIC MODULE, RESIDUES 42-354
    Organism Scientific: STREPTOMYCES LIVIDANS
    Organism Taxid: 1916
    Synonym: XYLANASE A, 1,4-BETA-D-XYLAN XYLANOHYDROLASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1XDN1Ligand/IonPIPERIDINE-3,4,5-TRIOL
2XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:44 , ASN A:45 , LYS A:48 , GLN A:88 , TRP A:266 , TRP A:274 , XDN A:1304 , HOH A:2690 , HOH A:2691 , HOH A:2692 , HOH A:2694 , HOH A:2695 , HOH A:2696 , HOH A:2697 , HOH A:2698 , HOH A:2700BINDING SITE FOR RESIDUE XYP A1303
2AC2SOFTWARELYS A:48 , HIS A:81 , TRP A:85 , ASN A:127 , GLU A:128 , GLN A:205 , GLU A:236 , TRP A:266 , TRP A:274 , XYP A:1303 , HOH A:2540 , HOH A:2698 , HOH A:2699 , HOH A:2700 , HOH A:2701 , HOH A:2702 , HOH A:2703BINDING SITE FOR RESIDUE XDN A1304

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:168 -A:201
2A:168 -A:201
3A:254 -A:260
4A:254 -A:260

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:81 -Thr A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V0K)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH10_1PS00591 Glycosyl hydrolases family 10 (GH10) active site.XYNA_STRLI270-280  1A:229-239

(-) Exons   (0, 0)

(no "Exon" information available for 1V0K)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:302
 aligned with XYNA_STRLI | P26514 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:302
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342  
           XYNA_STRLI    43 ESTLGAAAAQSGRYFGTAIASGRLSDSTYTSIAGREFNMVTAENEMKIDATEPQRGQFNFSSADRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGSSGARRDSNLQRSGNDWIEVAFRTARAADPSAKLCYNDYNVENWTWAKTQAMYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGAPASTYANVTNDCLAVSRCLGITVWGVRDSDSWRSEQTPLLFNNDGSKKAAYTAVLDALNGG 344
               SCOP domains d1v0ka_ A: Xylanase A, catalytic core                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1v0kA00 A:2-303 Glycosidases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains --Glyco_hydro_10-1v0kA01 A:4-300                                                                                                                                                                                                                                                                           --- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeee.............hhhhhh..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh.....eeee............hhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhh...eeeeee....hhhh.hhhhh..........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ---------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v0k A   2 ESTLGAAAAQSGRYFGTAIASGRLSDSTYTSIAGREFNMVTAENEMKIDATEPQRGQFNFSSADRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGSSGARRDSNLQRSGNDWIEVAFRTARAADPSAKLCYNDYNVENWTWAKTQAMYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGAPASTYANVTNDCLAVSRCLGITVWGVRDSDSWRSEQTPLLFNNDGSKKAAYTAVLDALNGG 303
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNA_STRLI | P26514)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0031176    endo-1,4-beta-xylanase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        XYNA_STRLI | P26514: 1e0v 1e0w 1e0x 1knl 1knm 1mc9 1od8 1v0l 1v0m 1v0n 1xas

(-) Related Entries Specified in the PDB File

1e0v XYLANASE 10A FROM SREPTOMYCES LIVIDANS. CELLOBIOSYL-ENZYME INTERMEDIATE AT 1.7 A
1e0w XYLANASE 10A FROM SREPTOMYCES LIVIDANS. NATIVE STRUCTURE AT 1.2 ANGSTROM RESOLUTION
1e0x XYLANASE 10A FROM SREPTOMYCES LIVIDANS. XYLOBIOSYL-ENZYME INTERMEDIATE AT 1.65 A
1knl STREPTOMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13
1knm STREPTOMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13 IN COMPLEXWITH LACTOSE
1mc9 STREPROMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13 IN COMPLEXWITH XYLOPENTAOSE
1od8 XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH XYLOBIO-ISOFAGOMINE LACTAM
1v0l XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH XYLOBIO-ISOFAGOMINE AT PH 5.8
1v0m XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH XYLOBIO-DEOXYNOJIRIMYCIN AT PH 7.5
1v0n XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH XYLOBIO-ISOFAGOMINE AT PH 7.5
1xas 1,4-BETA-D-XYLAN XYLANOHYDROLASE